Hi All, especially the seasoned CNCers,

I have A home build Grizzly Mini Mill with Gecko controller and Mach3 software. All was going well until I started using G59 to set tool Offset and G54 to set Work Offsets X + Gage, Y + Gage and Z + Gage. I presently am using a Non inverting X, and inverting Y and a Non-inverting Z port/pin setting in Mach3.

Background:
When I press the "Page Down" button, the Head goes towards the table. I think this is correct as Mach3 Zeros the Z axis.

When I press the "Left Arrow" button, the table goes in the Left or -X direction. I think this is also correct as Mach3 zeros the X axis.
When I press the "Up Arrow" button, the table goes in the +Y direction (into the Head). I think this is correct as Mach3 zeros the Y axis.

If this is not correct or what you use, Please respond with correction!

Here is my problem:
When I push "REF ALL HOME", the mill goes to (0,0,0) correctly.
When I set a G59 X,Y and Z, X is set to Some value, Y is set to some value and Z is set to some value (depends on when Tool Touch off is located). I save Work Offsets (or think I do) and exit Mach3. The values are lost and must be redone each time (Contrary to what I read on the screens which says "Make them permanent").
So I don't exit Mach3.
Instead, I set Part X to Gage thickness + X in the most Left position with work on the RIGHT (positive X direction). I believe the is X0 + Gage and G54 X is set to Gage thickness.
Next, I set Part Y to the closest to Y zero position with the work in the direction of +Y. I believe this is Y0 + Gage position.
Then I set Z to Top of Part + Gage.

At this point X = 0.0632, Y = 0.0632 and Z= 0.0016.

All looks great to me. At this point I save both Work Offset and Tool Offsets as I think they are correct. I then go to MIDI tab and enter "G0G90G54X0Y0" and the table moves in the -X and -Y direction by the value in G54 table (-0.0632, -0.0632) which doubles the offset to -0.125, -0.125. Very aggravating.

This is where I need help! The table should go to (0, 0) but instead goes to ( -0.125, -0.125). THIS IS MY PROBLEM!

Other information:
I have used the Port Pin assignment to invert the X and Y Direction. When I do this, the Mill zeros the part correctly but the Mill goes in the wrong direction to Reff All Home so is incorrectly set up.

Really need help so I've attached my NC file and my BobCAD-CAM Pat file.The attached file Grizzly... No-ATC is the BobCAD-CAM file and the Presentation... file the result nc file for Mach3.

I don't know if the values are off for the NC file and that isn't really an issue, I just included them for completeness.